N - mixture models by species

modelling N by site to get relative abundance

abundance by site will be used as a cov on predator occupancy

7 models evaluated, dot, jdt + jdtSQ, lure + jdt + jdtSQ


Species:      lagomorph



Metadata Summary:

N_sites N_counts N_detections rep_period iterations burnin thin
127 420 237 7 days 120000 20000 10



Detections by Year:

Yr 2016 2017 2018 2019 2020
sites 19 31 19 32 26
detections 24 47 43 80 43
N.dot.model 8 24 19 34 13



WAIC

Models by WAIC:
model description WAIC N.total.est
fm7 counts 5.683632 127
fm1 dot 1416.159272 98
fm3 lure 1416.862733 97
fm2 jdt 1417.331463 98
fm4 lure + jdt 1418.215634 98
fm5 jdt + jdtSq 1418.950661 98
fm6 lure + jdt + jdtSq 1421.163316 97



Model summaries:



model: fm1
dot



summary table

param covariate iters_ef mean mode hdi_89pct_lower hdi_89pct_upper bayes_P pct.density
p[1] NA 6512 0.128 0.117 0.07 0.18 0 1.001
p[2] NA 3444 0.078 0.077 0.05 0.11 0 1.001
p[3] NA 3761 0.053 0.052 0.03 0.07 0 1.001
p[4] NA 3627 0.072 0.069 0.05 0.09 0 1.001
p[5] NA 8123 0.103 0.098 0.07 0.13 0 1.001
lambda[1] NA 8106 0.492 0.403 0.20 0.78 0 1.001
lambda[2] NA 2972 1.048 0.927 0.52 1.49 0 1.001
lambda[3] NA 3036 1.293 1.064 0.62 1.92 0 1.001
lambda[4] NA 3988 1.303 1.203 0.78 1.79 0 1.001
lambda[5] NA 9527 0.583 0.525 0.31 0.86 0 1.001
N[46] NA 7311 1.665 1 1.00 3.00 0 1.0002
N[1] NA 9639 0.042 err 0.00 0.00 err err
N[43] NA 7277 0.227 err 0.00 1.00 err err
N[88] NA 8048 0.133 err 0.00 1.00 err err
N[100] NA 8389 1.058 err 1.00 1.00 err err

p[1]

p[2]

p[3]

p[4]

p[5]

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[46]

N[1]

N[43]

N[88]

N[100]







model: fm2
jdt



summary table

param covariate iters_ef mean mode hdi_89pct_lower hdi_89pct_upper bayes_P pct.density
alpha jdt 9447 0.004 0.006 -0.11 0.12 0.99853 0.5255
alpha0 NA 4272 -2.502 -2.48 -2.69 -2.30 0 1.001
lambda[1] NA 8319 0.661 0.596 0.29 1.00 0 1.001
lambda[2] NA 7679 1.014 0.991 0.62 1.39 0 1.001
lambda[3] NA 8443 0.936 0.857 0.55 1.33 0 1.001
lambda[4] NA 8044 1.212 1.186 0.82 1.61 0 1.001
lambda[5] NA 8601 0.680 0.629 0.36 0.98 0 1.001
N[47] NA 10000 0.133 err 0.00 1.00 err err
N[89] NA 10000 0.506 0 0.00 1.00 1 err
N[26] NA 10000 0.584 0 0.00 2.00 1 err
N[119] NA 10000 0.200 err 0.00 1.00 err err
N[65] NA 10000 0.126 err 0.00 1.00 err err

alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[47]

N[89]

N[26]

N[119]

N[65]

alpha relationship







model: fm3
lure



summary table

param covariate iters_ef mean mode hdi_89pct_lower hdi_89pct_upper bayes_P pct.density
alpha lure 10163 -0.029 -0.025 -0.16 0.11 0.92493 0.6364
alpha0 NA 4611 -2.504 -2.506 -2.69 -2.31 0 1.001
lambda[1] NA 8588 0.656 0.569 0.32 1.03 0 1.001
lambda[2] NA 8414 1.007 0.97 0.62 1.38 0 1.001
lambda[3] NA 8415 0.939 0.888 0.54 1.32 0 1.001
lambda[4] NA 7668 1.210 1.171 0.82 1.60 0 1.001
lambda[5] NA 8925 0.688 0.599 0.38 1.00 0 1.001
N[104] NA 9246 3.349 4 2.00 5.00 0 1.001
N[68] NA 10000 1.173 err 1.00 2.00 err err
N[102] NA 10000 0.031 err 0.00 0.00 err err
N[21] NA 9827 1.193 err 1.00 2.00 err err
N[112] NA 10000 0.040 err 0.00 0.00 err err

alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[104]

N[68]

N[102]

N[21]

N[112]

alpha relationship







model: fm4
lure + jdt



summary table

param covariate iters_ef mean mode hdi_89pct_lower hdi_89pct_upper bayes_P pct.density
alpha[1] lureDays 8080 -0.032 -0.033 -0.18 0.12 0.92326 0.637
alpha[2] julianDt 8130 0.015 0.015 -0.11 0.14 0.9759 0.5804
alpha0 NA 4688 -2.498 -2.496 -2.68 -2.31 0 1.001
lambda[1] NA 8537 0.646 0.639 0.29 0.98 0 1.001
lambda[2] NA 8374 1.005 0.972 0.63 1.39 0 1.001
lambda[3] NA 8943 0.932 0.836 0.52 1.31 0 1.001
lambda[4] NA 8084 1.201 1.137 0.82 1.60 0 1.001
lambda[5] NA 8840 0.685 0.64 0.37 0.98 0 1.001
N[104] NA 9394 3.382 3.002 2.00 5.00 0 1.001
N[45] NA 9670 1.740 1 1.00 3.00 0 1.0003
N[78] NA 9719 0.421 0 0.00 1.00 1 err
N[31] NA 10000 1.115 err 1.00 1.00 err err
N[5] NA 8870 1.887 2.003 1.00 3.00 0 1.0005

alpha[1]

alpha[2]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[104]

N[45]

N[78]

N[31]

N[5]







model: fm5
jdt + jdtSq



summary table

param covariate iters_ef mean mode hdi_89pct_lower hdi_89pct_upper bayes_P pct.density
alpha[1] julianDt 4014 0.072 0.074 -0.13 0.27 0.89961 0.7143
alpha[2] julianDtSq 4083 -0.086 -0.097 -0.29 0.12 0.80541 0.7476
alpha0 NA 4564 -2.503 -2.491 -2.69 -2.31 0 1.001
lambda[1] NA 8953 0.647 0.527 0.28 0.98 0 1.001
lambda[2] NA 8150 1.028 1.007 0.64 1.41 0 1.001
lambda[3] NA 9454 0.931 0.825 0.54 1.32 0 1.001
lambda[4] NA 7430 1.226 1.175 0.82 1.62 0 1.001
lambda[5] NA 9284 0.678 0.618 0.35 0.96 0 1.001
N[33] NA 9661 1.436 1 1.00 2.00 0 1.0001
N[21] NA 10000 1.196 err 1.00 2.00 err err
N[13] NA 8931 2.629 3 2.00 4.00 0 1.0009
N[56] NA 10000 0.046 err 0.00 0.00 err err
N[104] NA 8625 3.348 2.998 2.00 5.00 0 1.001

alpha[1]

alpha[2]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[33]

N[21]

N[13]

N[56]

N[104]

julian date relationship







model: fm6
lure + jdt + jdtSq



summary table

param covariate iters_ef mean mode hdi_89pct_lower hdi_89pct_upper bayes_P pct.density
alpha[1] lureDays 5545 -0.057 -0.058 -0.21 0.10 0.84323 0.7206
alpha[2] julianDt 3049 0.108 0.103 -0.12 0.33 0.73248 0.7765
alpha[3] julianDtSq 3217 -0.111 -0.135 -0.33 0.11 0.74073 0.7896
alpha0 NA 4423 -2.512 -2.489 -2.69 -2.31 0 1.001
lambda[1] NA 8268 0.624 0.554 0.28 0.95 0 1.001
lambda[2] NA 8178 1.020 0.954 0.62 1.38 0 1.001
lambda[3] NA 8695 0.925 0.86 0.53 1.30 0 1.001
lambda[4] NA 6869 1.228 1.172 0.80 1.61 0 1.001
lambda[5] NA 8332 0.697 0.617 0.37 1.01 0 1.001
N[10] NA 9820 0.103 err 0.00 0.00 err err
N[46] NA 10000 1.649 1 1.00 3.00 0 1.0002
N[23] NA 10000 0.354 0 0.00 1.00 1 err
N[31] NA 8427 1.122 err 1.00 2.00 err err
N[106] NA 10000 0.505 0 0.00 1.00 1 err

alpha[1]

alpha[2]

alpha[3]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[10]

N[46]

N[23]

N[31]

N[106]







model: fm7
counts



summary table

param covariate iters_ef mean mode hdi_89pct_lower hdi_89pct_upper bayes_P pct.density
alpha counts 8567 9.532 8.991 7.49 11.35 0 1.001
alpha0 NA 9239 -6.475 -6.099 -7.89 -5.06 0 1.001
lambda[1] NA 9109 0.984 0.858 0.42 1.53 0 1.001
lambda[2] NA 10000 0.992 0.935 0.60 1.34 0 1.001
lambda[3] NA 10000 0.994 0.929 0.56 1.44 0 1.001
lambda[4] NA 10360 0.994 0.937 0.65 1.36 0 1.001
lambda[5] NA 8870 0.974 0.866 0.47 1.43 0 1.001
N[50] NA 10000 1.004 err 1.00 1.00 err err
N[86] NA 0 1.000 err 1.00 1.00 err err
N[87] NA 0 1.000 err 1.00 1.00 err err
N[124] NA 10000 0.939 0 0.00 2.00 1 err
N[26] NA 10881 0.976 0 0.00 2.00 1 err

alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[50]

N[86]

## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[87]

## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[124]

N[26]

alpha relationship